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comparison MS2snoop.xml @ 3:c68c94865667 draft

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planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
author workflow4metabolomics
date Wed, 22 Jun 2022 13:07:01 +0000
parents a35fde23940e
children 856001213966
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2:a35fde23940e 3:c68c94865667
1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description> 2 <description>
3 MS1/MS2 spectra and associated adducts extraction and cleaning 3 MS1/MS2 spectra and associated adducts extraction and cleaning
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@TOOL_VERSION@">1.0.1</token> 6 <import>macros.xml</import>
7 <token name="@VERSION_SUFFIX@">1</token> 7 <token name="@TOOL_VERSION@">1.1.0</token>
8 <token name="@VERSION_SUFFIX@">0</token>
8 </macros> 9 </macros>
9 <edam_topics> 10 <edam_topics>
10 <edam_topic>topic_0091</edam_topic> 11 <edam_topic>topic_0091</edam_topic>
11 <edam_topic>topic_3370</edam_topic> 12 <edam_topic>topic_3370</edam_topic>
12 </edam_topics> 13 </edam_topics>
48 </command> 49 </command>
49 <inputs> 50 <inputs>
50 <param 51 <param
51 argument="--compound_txt" 52 argument="--compound_txt"
52 type="data" 53 type="data"
53 format="tabular,csv" 54 format="tabular,csv,tsv"
54 label="list of compounds" 55 label="list of compounds"
55 help="The table must fit the format: col1=Name of molecule, col2=m/z, col3=retention time" 56 help="The table must fit the format: col1=Name of molecule, col2=m/z, col3=retention time"
56 /> 57 />
57 <param 58 <param
58 argument="--peaklist_frag_tsv" 59 argument="--peaklist_frag_tsv"
59 type="data" 60 type="data"
60 format="tabular,csv" 61 format="tabular,csv,tsv"
61 label="MSpurity fragments file" 62 label="MSpurity fragments file"
62 /> 63 />
63 <param 64 <param
64 argument="--peaklist_preco_tsv" 65 argument="--peaklist_preco_tsv"
65 type="data" 66 type="data"
66 format="tabular,csv" 67 format="tabular,csv,tsv"
67 label="MSpurity precursors file" 68 label="MSpurity precursors file"
68 /> 69 />
69 <param 70 <param
70 argument="--tolmz" 71 argument="--tolmz"
71 type="float" 72 type="float"
148 <test> 149 <test>
149 <param name="compound_txt" value="compounds_pos.txt" /> 150 <param name="compound_txt" value="compounds_pos.txt" />
150 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> 151 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
151 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> 152 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
152 <output name="frag_result_txt" file="compound_fragments_result.txt" /> 153 <output name="frag_result_txt" file="compound_fragments_result.txt" />
154 <assert_stdout>
155 <expand macro="has_regular_stdout"/>
156 <expand macro="has_not_verbose_stdout"/>
157 <expand macro="has_not_debug_stdout"/>
158 </assert_stdout>
159 </test>
160 <test>
161 <param name="compound_txt" value="compounds_pos.txt" />
162 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
163 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
164 <param name="verbose" value="--verbose" />
165 <output name="frag_result_txt" file="compound_fragments_result.txt" />
166 <assert_stdout>
167 <expand macro="has_regular_stdout"/>
168 <expand macro="has_verbose_stdout"/>
169 <expand macro="has_not_debug_stdout"/>
170 </assert_stdout>
171 </test>
172 <test>
173 <param name="compound_txt" value="compounds_pos.txt" />
174 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
175 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
176 <param name="debug" value="--debug" />
177 <output name="frag_result_txt" file="compound_fragments_result.txt" />
178 <assert_stdout>
179 <expand macro="has_smol_stdout"/>
180 <expand macro="has_debug_stdout"/>
181 <expand macro="has_not_verbose_stdout"/>
182 </assert_stdout>
183 </test>
184 <test>
185 <param name="compound_txt" value="compounds_pos.txt" />
186 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
187 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
188 <param name="debug" value="--debug" />
189 <param name="verbose" value="--verbose" />
190 <output name="frag_result_txt" file="compound_fragments_result.txt" />
191 <assert_stdout>
192 <expand macro="has_smol_stdout"/>
193 <expand macro="has_debug_stdout"/>
194 <expand macro="has_smol_verbose_stdout"/>
195 </assert_stdout>
196 </test>
197 <test>
198 <param name="compound_txt" value="compounds_pos.csv" />
199 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
200 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
201 <output name="frag_result_txt" file="compound_fragments_result.txt" />
202 <assert_stdout>
203 <expand macro="has_regular_stdout"/>
204 <expand macro="has_not_verbose_stdout"/>
205 <expand macro="has_not_debug_stdout"/>
206 </assert_stdout>
207 </test>
208 <test>
209 <param name="compound_txt" value="compounds_pos.csv" />
210 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
211 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
212 <param name="verbose" value="--verbose" />
213 <output name="frag_result_txt" file="compound_fragments_result.txt" />
214 <assert_stdout>
215 <expand macro="has_regular_stdout"/>
216 <expand macro="has_verbose_stdout"/>
217 <expand macro="has_not_debug_stdout"/>
218 </assert_stdout>
219 </test>
220 <test>
221 <param name="compound_txt" value="compounds_pos.csv" />
222 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
223 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
224 <param name="debug" value="--debug" />
225 <output name="frag_result_txt" file="compound_fragments_result.txt" />
226 <assert_stdout>
227 <expand macro="has_smol_stdout"/>
228 <expand macro="has_debug_stdout"/>
229 <expand macro="has_not_verbose_stdout"/>
230 </assert_stdout>
231 </test>
232 <test>
233 <param name="compound_txt" value="compounds_pos.csv" />
234 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
235 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
236 <param name="debug" value="--debug" />
237 <param name="verbose" value="--verbose" />
238 <output name="frag_result_txt" file="compound_fragments_result.txt" />
239 <assert_stdout>
240 <expand macro="has_smol_stdout"/>
241 <expand macro="has_debug_stdout"/>
242 <expand macro="has_smol_verbose_stdout"/>
243 </assert_stdout>
153 </test> 244 </test>
154 </tests> 245 </tests>
155 <help><![CDATA[ 246 <help><![CDATA[
156 .. class:: infomark 247 .. class:: infomark
157 248
161 252
162 --------------------------------------------------- 253 ---------------------------------------------------
163 254
164 255
165 ============== 256 ==============
166 MS2 validation 257 MS2 validation
167 ============== 258 ==============
168 259
169 ----------- 260 -----------
170 Description 261 Description
171 ----------- 262 -----------